Background: Early and prolonged prone positioning (PP) could reduce the mortality in patients with moderate to severe ARDS, however, factors associated with mortality in the intensive care unit (ICU) remain unclear. The aim of this study is to identified factors associated with mortality and create the prognostic score in patients with ARDS who underwent early and prolonged PP. Methods: This retrospective study included patients with moderate to severe ARDS admitted to the intensive care unit (ICU) from January 2015 to June 2018 in a tertiary referral center in Taiwan and who received early and prolonged PP. Demographic data, disease severity score, comorbidities, and clinical outcomes were recorded. Univariate and multivariate regression models were used to estimate the odds ratio (OR) of ICU mortality. Receiver operating characteristic (ROC) curve analysis were performed to identify the cutoff value of parameters. Results: A total of 116 patients were enrolled. In the multivariate analysis, three factors were significantly associated with mortality: renal replacement therapy (RRT; OR: 3.38, 1.55–7.36), malignant comorbidity (OR: 7.42, 2.06–26.70), and noninfluenza-related ARDS (OR: 3.78, 1.07–13.29). Age, RRT, noninfluenza-related ARDS, malignant comorbidity, and APACHE II score were included in a composite prone score, which demonstrated an area under the curve of 0.816 for predicting mortality risk. The mortality risk in ICU was 27.1% in the low-risk group (prone score: 0–2) and 84.2% in the high-risk group (prone score: 3–5). Conclusions: For patients with moderate to severe ARDS even receiving early and prolonged PP in ICU, poor prognostic factors were age, RRT, malignant comorbidity, noninfluenza-related ARDS, and higher APACHE II score. High mortality should be informed to the family of patient if their prone score was more than 3 points.